Gel Electrophoresis Online Simulation http://learn.genetics.utah.edu/content/lab
ID: 276918 • Letter: G
Question
Gel Electrophoresis Online Simulation
http://learn.genetics.utah.edu/content/labs/gel/
Go to the website above to answer the questions below. You will have to navigate through the electrophoresis interactive/simulation and it is quite obnoxious with beeps and noises so use your headphones if you like.
Questions:
What is electrophoresis used for?
What is the material of the gel similar to?
Why is electricity required for electrophoresis to work?
Describe how the DNA fragments migrate through the gel matrix.
What moves farther – shorter or longer fragments? Why?
If two lanes had bands/fragments at the same location could you assume that the DNA at these locations was the same length? Why or why not?
Run the Gel
Follow the instructions to run the gel.
What ingredients/materials are necessary to perform an electrophoresis experiment?
Why do you need to use buffer?
Why do you need a microwave? Could you use something else? What?
What is the tape for on the gel casting tray?
What is the comb for?
What is the buffer for in the chamber?
Why would you need a clean pipette tip?
What is the DNA size standard for?
What would happen if you switched the black and red wires?
Are bubbles good? How/why could they be helpful?
Does DNA move toward red or black? Why is this?
What is the point of the Ethidium Bromide?
What is the UV box for?
Explanation / Answer
Hi Answer:
What is electrophoresis used for?
Answer: The electrophoresis is used separate out the charged biomolecules of different size/length in the presence of electric current. The biomolecules may DNA, RNA or protein etc.
What is the material of the gel similar to?
Answer: The gel is the filter which is similar to a sponge having a large number of small pores.
Why is electricity required for electrophoresis to work?
Answer: The electric current push the charged biomolecules towards the opposite side for example DNA have a negative charge when we pass electric current to DNA loaded gel then DNA start moving towards positive electrode and it separates the fragments of different length.
Describe how the DNA fragments migrate through the gel matrix.
Answer: In the presence of electric current DNA fragment having a small size or low molecular weight move faster whereas the fragments having high molecular weight and larger size move slower.
What moves farther – shorter or longer fragments? Why?
Answer: Shorter fragments move faster whereas larger moves slower due to their molecular weight, heavy the fragment slower the movement and vice a versa.
If two lanes had bands/fragments at the same location could you assume that the DNA at these locations was the same length? Why or why not?
Answer: Yes it the two bands present at the same location we can say that the molecular weight and length of these fragments is similar.
Run the Gel
What ingredients/materials are necessary to perform an electrophoresis experiment?
Answer: Main ingredients are: Gel electrophoresis unit with power supply, Agarose gel, microwave oven, flask, gel comb biomolecules such DNA or RNA, Gel loading dye, TAE Buffer, ethidium bromide, molecular weight marker, UV box
Why do you need to use a buffer?
Answer: To run current through gel we need a liquid medium and the TAE buffer used in this case is the excellent liquid which helps in the running the electric current through the gel.
Why do you need a microwave? Could you use something else? What?
Answer: To heat up the agarose powder mixed with TAE buffer to polymerize it as agarose gel. Yes, we can also use heating plate but it took longer .
What is the tape for on the gel casting tray?
Answer: To secure the gates of the gel casting tray so that melted agarose did not flow out the tray during gel casting gel.
What is the comb for?
Answer: The comb is used to make the uniform wells in the polymerized gel. It is inserted in the melted (hot) agarose at the time of starting of the casting of gel in the tray after polymerization the comb form small uniform size wells on the polymerized gel.
What is the buffer for in the chamber?
Answer: TAE buffer is used as the electrophoretic buffer used to flow the electric current through the agarose gel.
Why would you need a clean pipette tip?
Answer: To avoid unwanted material is not loaded along with DNA on the agarose gel which may binds to DNA and change its size and produce fake results.
What is the DNA size standard for?
Answer: To determine the size of the DNA fragments which is to be separated by the experiments. DNA size standard is used as reference material to compare the size of DNA fragments.
What would happen if you switched the black and red wires?
Answer: the current will start flowing through the agarose gel.
Are bubbles good? How/why could they be helpful?
Answer: No bubbles are not good. They interfere with the flow of current and may cause the abnormal flow of electric current.
Does DNA move toward red or black? Why is this?
Answer: In electrophoresis, the red end is the positively charged anode and black end is the negative charge cathode. DNA will move towards the red end as DNA has a negative charge and it always moves towards positive end i.e. towards red.
What is the point of the Ethidium Bromide?
Answer: Ethidium bromide is an intercalating agent and commonly use as a fluorescent tag to detect the DNA during gel electrophoresis because it illuminates in the presence of UV light.
What is the UV box for?
Answer: To visualize the fluorescently tagged DNA fragments.
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